This invention relates to a gene which has been associated with breast and ovarian cancer where the gene is found to be mutated. More specifically, this invention relates to a coding sequence of the BRCA1 gene, BRCA1(omi4), isolated from human subjects which defines a new haplotype.
It has been estimated that about 5-10% of breast cancer is inherited Rowell, et al., American Journal of Human Genetics, 55:861-865 (1994). Located on chromosome 17, BRCA1 is the first gene identified to be conferring increased risk for breast and ovarian cancer. Miki et al., Science, 266:66-71 (1994). Mutations in this xe2x80x9ctumor suppressorxe2x80x9d gene are thought to account for roughly 45% of inherited breast cancer and 80-90% of families with increased risk of early onset breast and ovarian cancer. Easton et al., American Journal of Human Genetics, 52:678-701 (1993).
Locating one or more mutations in the BRCA1 region of chromosome 17 provides a promising approach to reducing the high incidence and mortality associated with breast and ovarian cancer through the early detection of women at high risk. These women, once identified, can be targeted for more aggressive prevention programs. Screening is carried out by a variety of methods which include karyotyping, probe binding and DNA sequencing.
In DNA sequencing technology, genomic DNA is extracted from whole blood and the coding sequences of the BRCA1 gene are amplified. The coding sequences might be sequenced completely and the results are compared to the DNA sequence of the gene. Alternatively, the coding sequence of the sample gene may be compared to a panel of known mutations or other screening procedure before completely sequencing the gene and comparing it to a normal sequence of the gene.
If a mutation in the BRCA1 coding sequence is found, it may be possible to provide the individual with increased expression of the gene through gene transfer therapy. It has been demonstrated that the gene transfer of the BRCA1 coding sequence into cancer cells inhibits their growth and reduces tumorigenesis of human cancer cells in nude mice. Jeffrey Holt and his colleagues conclude that the product of BRCA1 expression is a secreted tumor growth inhibitor, making BRCA1 an ideal gene for gene therapy studies. Transduction of only a moderate percentage of tumor cells apparently produces enough growth inhibitor to inhibit all tumor cells. Arteaga and Holt, Cancer Research, 56: 1098-1103 (1996), Holt, et al., Nature Genetics, 12: 298-302 (1996). The observation of Holt et al, that the BRCA1 growth inhibitor is a secreted protein leads to the possible use of infection of the BRCA1 growth inhibitor into the area of the tumor for tumor suppression.
The BRCA1 gene is divided into 24 separate exons. Exons 1 and 4 are noncoding, in that they are not part of the final functional BRCA1 protein product. The BRCA1 coding sequence spans roughly 5600 base pairs (bp). Each exon consists of 200-400 bp, except for exon 11 which contains about 3600 bp. To sequence the coding sequence of the BRCA1 gene, each exon is amplified separately and the resulting PCR products are sequenced in the forward and reverse directions. Because exon 11 is so large, we have divided it into twelve overlapping PCR fragments of roughly 350 bp each (segments xe2x80x9cAxe2x80x9d through xe2x80x9cLxe2x80x9d of BRCA1 exon 11).
Many mutations and polymorphisms have already been reported in the BRCA1 gene. A world wide web site has been built to facilitate the detection and characterization of alterations in breast cancer susceptibility genes. Such mutations in BRCA1 can be accessed through the Breast Cancer Information Core (BIC) at: www.nchgr.nih.gov/dir/lab_transfer/bic. This data site became publicly available on Nov. 1, 1995. Friend, et al. Nature Genetics, 11:238, (1995).
The genetics of Breast/Ovarian Cancer Syndrome is autosomal dominant with reduced penetrance. In simple terms, this means that the syndrome runs through families: (1) both sexes can be carriers (mostly women get the disease but men can both pass it on and occasionally get breast cancer); (2) most generations will likely have breast cancer; (3) occasionally women carriers either die young before they have the time to manifest disease (and yet have offspring who get it) or they never develop breast or ovarian cancer and die of old age (the latter people are said to have xe2x80x9creduced penetrancexe2x80x9d because they never develop cancer). Pedigree analysis and genetic counseling is absolutely essential to the proper workup of a family prior to any lab work.
Until recently, only a single coding sequence for the BRCA1 gene has been available for comparison to patient samples. That sequence is available as GENBANK Accession Number U14680. Recently another sequence has been made known in U.S. Pat. No. 5,654,155. There is a need in the art, to have available a coding sequence which is the BRCA1 coding sequence found in a portion of the normal population in order to determine whether or not a patient""s BRCA1 gene sequence is mutant with increased succeptibility for cancer or a different normal sequence with no such succeptability. This will make it possible for true mutations to be easily identified or differentiated from naturally occurring sequence variations such as polymorphisms. Identification of mutations of the BRCA1 gene and protein allow more widespread diagnostic screening for hereditary breast and ovarian cancer than is currently possible and also have utility in gene therapy, protein replacement therapy and diagnosis.
Knowing the coding sequences which do not represent a higher susceptibility to an individual for cancer will reduce the likelihood of misinterpreting a xe2x80x9csequence variationxe2x80x9d found in the population (i.e. polymorphism) with a pathologic xe2x80x9cmutationxe2x80x9d (i.e. causes disease in the individual or puts the individual at a high risk of developing the disease). With large interest in breast cancer predisposition testing, misinterpretation is particularly worrisome. People who already have breast cancer are asking the clinical question: xe2x80x9cis my disease caused by a heritable genetic mutation?xe2x80x9d The relatives of the those with breast cancer are asking the question: xe2x80x9cAm I also a carrier of the mutation my relative has? Thus, is my risk increased, and should I undergo a more aggressive surveillance program.xe2x80x9d
The present invention is based on the isolation of a coding sequence of the BRCA1 gene found in human individuals.
It is an object of the invention to define a haplotype of a BRCA1 gene, BRCA1(omi4), in normal individuals which does not correspond to increased cancer susceptibility.
It is another object of this invention to sequence a BRCA1 gene or portion thereof and compare it to the newly discovered haplotype, BRCA1(omi4), to determine whether a sequence variation noted represents a polymorphism or a potentially harmful mutation.
It is another object of the invention to provide a protein sequence coded for by the coding sequence of the BRCA1 gene.
It is another object of the invention to provide a list of the codon pairs which occur at each of seven polymorphic points on the BRCA1 gene.
It is another object of the invention to provide a method wherein the BRCA1 gene, or parts thereof, are amplified with one or more oligonucleotide primers.
It is another object of this invention to provide a method of identifying individuals who carry no mutation(s) of the BRCA1 coding sequence and therefore have no increased genetic susceptibility to breast or ovarian cancer based on their BRCA1 genes.
It is another object of this invention to provide a method of identifying a mutation leading to an increased genetic susceptibility to breast or ovarian cancer.
It is another object of the invention to encompass prokaryotic or eukaryotic host cells comprising an expression vector having a DNA sequence that encodes for all or a fragment of the BRCA1(omi4) protein, a BRCA1(omi4) polypeptide, or a functional equivalent thereof.
It is another object of the invention to encompass all or fragments of BRCA1(omi4) protein, BRCA1(omi4) polypeptides, and functional equivalents thereof.
It is another object of the invention to encompass an anti-BRCA1(omi4) protein antibody or an antibody using a BRCA1(omi4) polypeptide or a functional equivalent thereof as an immunogen.
There is a need in the art for sequences of the BRCA1 gene and for the protein sequences of BRCA1 from normal individuals who are not at risk for increased susceptibility for cancer. In order to determine whether a sample from a patient suspected of containing a BRCA1 mutation actually has the mutation, the patient""s BRCA1 DNA and/or amino acid sequence need to be compared to all known normal BRCA1 sequences. Failure to compare the sequence obtained to all naturally occurring normal sequences may result in reporting a sample as containing a potentially harmful mutation when it is a polymorphism without clinical significance.
A person skilled in the art of genetic susceptibility testing will find the present invention useful for:
a) identifying individuals having a BRCA1 gene with no coding mutations, who therefore cannot be said to have an increased genetic susceptibility to breast or ovarian cancer from their BRCA1 genes;
b) avoiding misinterpretation of polymorphisms found in the BRCA1 gene;
c) determining the presence of a previously unknown mutation in the BRCA1 gene.
d) identifying a mutation which increases the genetic susceptibility to breast or ovarian cancer.
e) probing a human sample of the BRCA1 gene by allele to determine the presence or absence of either polymorphic allels or mutations;
f) performing gene therapy with the BRCA1(omi4) gene sequence or parts thereof;
g) performing protein replacement therapy with the BRCA1(omi4) protein sequence or a functional equivalent thereof; and
(h) performing diagnosis with a reagent derived from the BRCA1(omi4) DNA and protein sequence.
Definitions
The following definitions are provided for the purpose of understanding this invention.
xe2x80x9cBreast and Ovarian cancerxe2x80x9d is understood by those skilled in the art to include breast and ovarian cancer in women and also breast and prostate cancer in men. BRCA1 is also associated with genetic susceptibility to colon cancer. Therefore, claims in this document which recite breast and/or ovarian cancer refer to breast, ovarian, prostate, and colon cancers in men and women.
xe2x80x9cCoding sequencexe2x80x9d or xe2x80x9cDNA coding sequencexe2x80x9d refers to those portions of a gene which, taken together, code for a peptide (protein), or which nucleic acid itself has function.
xe2x80x9cProteinxe2x80x9d or xe2x80x9cpeptidexe2x80x9d refers to a sequence of amino acids which has function.
xe2x80x9cBRCA1(omi4)xe2x80x9d refers to the BRCA1(omi4) coding sequences. The BRCA1(omi4) gene refers to the gene encoding the coding sequence and its introns (particularly the splice sites adjacent to the exons) and regulatory sequences. In the present invention, the gene or its fragments are generally isolated from the host cells and in a non-chromosomal form.
xe2x80x9cBRCA1(omi4)xe2x80x9d refers to SEQ ID NO:1, a coding sequence for the BRCA1 gene. The coding sequence was found by end to end sequencing of a BRCA1 allele from an individual. The sequenced gene was found not to contain any mutations. BRCA1(omi4) defines a new haplotype. This sequence variation is believed to be an allele whose haplotype does not indicate an increased risk for cancer.
xe2x80x9cPrimerxe2x80x9d as used herein refers to an oligonucleotide comprising about 20 or more nucleotides having a sequence complementary to the BRCA1 gene. Other primers which can be used for primer hybridization will be known or readily ascertainable to those of skill in the art.
xe2x80x9cGenetic susceptibilityxe2x80x9d refers to the susceptibility to breast or ovarian cancer due to the presence of a mutation in the BRCA1 gene.
xe2x80x9cTarget polynucleotidexe2x80x9d refers to the nucleic acid sequence of interest e.g., the BRCA1 encoding polynucleotide.
xe2x80x9cCoding sequencexe2x80x9d or xe2x80x9cDNA coding sequencexe2x80x9d refers to those portions of a gene which, taken together, code for a peptide (protein), or for which the nucleic acid itself has function.
xe2x80x9cConsensusxe2x80x9d means the most commonly occurring in the population.
xe2x80x9cConsensus genomic sequencexe2x80x9d means the allele of the target gene which occurs with the greatest frequency in a population of individuals having no family history of disease associated with the target gene.
xe2x80x9cSubstantially complementary toxe2x80x9d refers to a probe or primer sequences which hybridize to the sequences provided under stringent conditions and/or sequences having sufficient homology with BRCA1 sequences, such that the allele specific oligonucleotide probe or primers hybridize to the BRCA1 sequences to which they are complimentary.
xe2x80x9cHaplotypexe2x80x9d refers to a series of specific alleles within a gene along a chromosome.
xe2x80x9cIsolatedxe2x80x9d as used herein refers to substantially free of other poly or oligonucleic acids, proteins, lipids, carbohydrates or other materials with which they may be associated. Such association is typically either in cellular material or in a synthesis medium.
xe2x80x9cMutationxe2x80x9d refers to a base change or a gain or loss of base pair(s) in a DNA sequence, which results in a DNA sequence which codes for a non-functioning protein or a protein with substantially reduced or altered function.
xe2x80x9cPolymorphismxe2x80x9d refers to a base change in a DNA sequence which is not associated with known pathology.
xe2x80x9cBiological samplexe2x80x9d refers to a polynucleotide containing sample originally from a biological source. The sample may be from a living, dead or even archeological source from a variety of tissues and cells. Examples include: body fluid [blood (leukocytes), urine (epithelial cells), saliva, breast milk, menstrual flow, cervical and vaginal secretions, etc.] skin, hair roots/follicle, mucus membrane (e.g. buccal or tongue cell scrapings), cervicovaginal cells (from PAP smear, etc.), lymphatic tissue, internal tissue (normal or tumor).
xe2x80x9cVectorxe2x80x9d refers to any polynucleotide which is capable of self replication or inducing integration into a self replicating polynucleotide. Examples include polynucleotides containing an origin or replication or an integration site. Vectors may be intergrated into the host cell""s chromosome or form an autonomously replicating unit.
xe2x80x9cA BRCA1 tumor growth inhibitorxe2x80x9d refers to a molecule such as, the BRCA1(omi4) protein, a homologous polypeptide, or a functional equivalent thereof that is effective for preventing the formation of, reducing or eliminating a transformed or malignant phenotype of breast or ovarian cancer cells.
xe2x80x9cA BRCA1(omi4) polypeptidexe2x80x9d refers to a BRCA1 polypeptide either directly derived from the BRCA1(omi4) protein, or homologous to the BRCA1(omi4) protein, or a fusion protein thereof.
xe2x80x9cA functional equivalentxe2x80x9d refers to a molecule including an unnatural BRCA1(omi4) polypepide, a drug, or a natural product which retains substantial biological activity as the native BRCA1(omi4) protein in preventing, diagnosing, monitoring, and treating breast and ovarian cancer.
The invention in several of its embodiments includes: an isolated DNA sequence of the BRCA1 coding sequence as set forth in SEQ ID NO:1, a protein sequence of the BRCA1 protein as set forth in SEQ ID NO:2, a method of identifying individuals having a mutant or normal BRCA1 gene, a method of detecting an increased genetic susceptibility to breast and ovarian cancer in an individual resulting from the presence of a mutation in the BRCA1 coding sequence, a method of performing gene therapy to prevent or treat a tumor, and a method of protein replacement therapy to prevent or treat a tumor.
While a different BRCA1 haplotype which appears to encode for the same amino acid sequence has very recently been published (Shattuck-Eidens et al., J. Am. Med. Assn. 278(15) 1242-1250 (1997)), applicants have determined the complete nucleotide and amino acid sequence for BRCA1(omi4) as defined in SEQ ID NO:1 and SEQ ID NO:2 and reduced the invention to practice before this publication date.
The BRCA1(omi4) haplotype is described as encompassing the alternative alleles found at polymorphic nucleotide sites 2201, 2430, 2731, 3232, 3667, 4427, and 4956. For comparison, the haplotype that is GENBANK #Accession Number U14680 is designated as haplotype #1 in TABLE I. The haplotype of U.S. Pat. No. 5,654,155, is designated as haplotype #2. Other published variations at these seven nucleotide sites are also provided. It should be noted that it has been published (Shattuck-Eidens et al., J. Am. Med. Assn. 278(15) 1242-1250 (1997)) that the polymorphism occurs at 3233 rather than 3232. This difference appears to be the result of an equipment error or the number accorded to the sequence as when the sequencing is performed by experienced technologists and manually interpretated independently, the polymorphism occurs at nucleotide position 3232.
Sequencing
Any nucleic acid specimen, in purified or non-purified form, can be utilized as the starting nucleic acid, providing it contains, or is suspected of containing, the specific nucleic acid sequence containing a polymorphic locus. Thus, the process may amplify, for example, DNA or RNA, including messenger RNA and cDNA, wherein DNA or RNA may be single stranded or double stranded. In the event that RNA is to be used as a template, enzymes, and/or conditions optimal for reverse transcribing the template to DNA would be utilized. In addition, a DNA-RNA hybrid which contains one strand of each may be utilized. A mixture of nucleic acids may also be employed, or the nucleic acids produced in a previous method, such as an amplification reaction using the same or different primers may be so utilized. See the BIC for representative primers which may be used for PCR amplification. The specific nucleic acid sequence to be amplified, i.e., the polymorphic locus, may be a fraction of a larger molecule or can be present initially as a discrete molecule, so that the specific sequence constitutes the entire nucleic acid. A variety of amplification techniques may be used such as ligating the DNA sample or fragments thereof to a vector capable of replication or incorporation into a replicating system thereby increasing the number of copies of DNA suspected of containing at least a portion of the BRCA1 gene. Amplification techniques include so called xe2x80x9cshot gun cloning.xe2x80x9d It is not necessary that the sequence to be amplified be present initially in a pure form; it may be a minor fraction of a complex mixture, such as contained in whole human DNA.
It should be noted that one need not sequence the entire coding region or even an entire DNA fragment in order to determine whether or not a mutation is present. For example, when a mutation is known in one family member, it is sufficient to determine the sequence at only the mutation""site by sequencing or by other mutation detection system, such as allele-specific oligonucleotide (ASO), when testing other family members.
DNA utilized herein may be extracted from a body sample, such as blood, tissue material and other biological samples by a variety of techniques such as that described by Maniatis, et. al. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., p. 280-281, (1982). If the extracted sample is impure, it may be treated before amplification with an amount of a reagent effective to open the cells, or animal cell membranes of the sample, and to expose and/or separate the strand(s) of the nucleic acid(s). This lysing and nucleic acid denaturing step to expose and separate the strands will allow amplification to occur much more readily.
For amplification by cloning, the DNA containing sample may be cleaved into fragments by a restriction endonuclease or by shearing by passing the DNA containing mixture through a 25 gauge needle from a syringe to prepare 1-1.5 kb fragments. The fragments are then ligated to a cleaved vector, (virus, plasmid, transposon, cosmid etc.) and then the recombinant vector so formed is then replicated in a manner typical for that vector.
For a PCR amplification, the deoxyribonucleotide triphosphates DATP, dCTP, dGTP, and dTTP are added to the synthesis mixture, either separately or together with the primers, in adequate amounts and the resulting solution is heated to about 90xc2x0-100xc2x0 C. from about 1 to 10 minutes, preferably from 1 to 4 minutes. After this heating period, the solution is allowed to cool to a temperature which is preferable for primer hybridization. To the cooled mixture is added an appropriate agent for effecting the primer extension reaction (called herein xe2x80x9cagent for polymerizationxe2x80x9d), and the reaction is allowed to occur under conditions known in the art. The agent for polymerization may also be added together with the other reagents if it is heat stable. This synthesis (or amplification) reaction may occur at room temperature up to a temperature above which the agent for polymerization no longer functions. Thus, for example, if DNA polymerase is used as the agent, the temperature is generally no greater than about 40xc2x0 C. When using thermostable DNA polymerase such as Taq, higher temperatures may be used.
The primers used to carry out this invention embrace oligonucleotides of sufficient length and appropriate sequence to provide initiation of DNA polymerization. Environmental conditions conducive to synthesis include the presence of nucleoside triphosphates and an agent for polymerization, such as DNA polymerase, and a suitable temperature and pH. The primer is preferably single stranded for maximum efficiency in amplification, but may be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the inducing agent for polymerization. The exact length of primer will depend on many factors, including temperature, buffer, and nucleotide composition. The oligonucleotide primer typically contains 12-20 or more nucleotides, although it may contain fewer nucleotides.
Primers used to carry out this invention are designed to be substantially complementary to each strand of the genomic locus to be amplified. This means that the primers must be sufficiently complementary to hybridize with their respective strands under conditions which allow the agent for polymerization to perform. In other words, the primers should have sufficient complementarity with the 5xe2x80x2 and 3xe2x80x2 sequences flanking the mutation to hybridize therewith and permit amplification of the genomic locus.
Oligonucleotide primers of the invention are employed in the amplification process which is an enzymatic chain reaction that produces exponential quantities of polymorphic locus relative to the number of reaction steps involved. Typically, one primer is complementary to the negative (xe2x88x92) strand of the polymorphic locus and the other is complementary to the positive (+) strand. Annealing the primers to denatured nucleic acid followed by extension with an enzyme, such as the large fragment of DNA polymerase I (Klenow) and nucleotides, results in newly synthesized + and xe2x88x92 strands containing the target polymorphic locus sequence. Because these newly synthesized sequences are also templates, repeated cycles of denaturing, primer annealing, and extension results in exponential production of the region (i.e., the target polymorphic locus sequence) defined by the primers. The product of the chain reaction is a discreet nucleic acid duplex with termini corresponding to the ends of the specific primers employed.
The oligonucleotide primers of the invention may be prepared using any suitable method, such as conventional phosphotriester and phosphodiester methods or automated embodiments thereof. In one such automated embodiment, diethylphosphoramidites are used as starting materials and may be synthesized as described by Beaucage, et al., Tetrahedron Letters, 22:1859-1862, 1981. One method for synthesizing oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,066.
The xe2x80x9cagent for polymerizationxe2x80x9d may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes. Suitable enzymes for this purpose include, for example, E. coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase, polymerase muteins, reverse transcriptase, other enzymes, including heat-stable enzymes (i.e., those enzymes which perform primer extension after being subjected to temperatures sufficiently elevated to cause denaturation), such as Taq polymerase. Suitable enzyme will facilitate combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each polymorphic locus nucleic acid strand. Generally, the synthesis will be initiated at the 3xe2x80x2 end of each primer and proceed in the 5xe2x80x2 direction along the template strand, until synthesis terminates, producing molecules of different lengths.
The newly synthesized strand and its complementary nucleic acid strand will form a double-stranded molecule under hybridizing conditions described above and this hybrid is used in subsequent steps of the process. In the next step, the newly synthesized double-stranded molecule is subjected to denaturing conditions using any of the procedures described above to provide single-stranded molecules.
The steps of denaturing, annealing, and extension product synthesis can be repeated as often as needed to amplify the target polymorphic locus nucleic acid sequence to the extent necessary for detection. The amount of the specific nucleic acid sequence produced will accumulate in an exponential fashion. Amplification is described in PCR. A Practical Approach, ILR Press, Eds. M. J. McPherson, P. Quirke, and G. R. Taylor, 1992.
The amplification products may be detected by Southern blots analysis, without using radioactive probes. In such a process, for example, a small sample of DNA containing a very low level of the nucleic acid sequence of the polymorphic locus is amplified, and analyzed via a Southern blotting technique or similarly, using dot blot analysis. The use of non-radioactive probes or labels is facilitated by the high level of the amplified signal. Alternatively, probes used to detect the amplified products can be directly or indirectly detectably labeled, for example, with a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator or an enzyme. Indirect labeling may be performed by binding a ligand or receptor to the probe, primer or amplified product and then contacting it with a labeled corresponding receptor or ligand. Those of ordinary skill in the art will know of other suitable labels for binding to the probe, or will be able to ascertain such, using routine experimentation.
Sequences amplified by the methods of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a specific DNA sequence such as PCR, oligomer restriction (Saiki, et. al., Bio/Technology, 3:1008-1012, 1985), allele-specific oligonucleotide (ASO) probe analysis (Conner, et. al., Proc. Natl. Acad. Sci. U.S.A., 80:278, 1983), oligonucleotide ligation assays (OLAs) (Landgren, et. al., Science, 241:1007, 1988), RFLP and the like. Molecular techniques for DNA analysis have been reviewed (Landgren, et. al., Science, 242:229-237, 1988).
Preferably, the method of amplifying is by PCR, as described herein and as is commonly used by those of ordinary skill in the art. Alternative methods of amplification have been described and can also be employed as long as the BRCA1 locus amplified by PCR using primers of the invention is similarly amplified by the alternative means. Such alternative amplification systems include but are not limited to self-sustained sequence replication, which begins with a short sequence of RNA of interest and a T7 promoter. Reverse transcriptase copies the RNA into cDNA and degrades the RNA, followed by reverse transcriptase polymerizing a second strand of DNA. Another nucleic acid amplification technique is nucleic acid sequence-based amplification (NASBA) which uses reverse transcription and T7 RNA polymerase and incorporates two primers to target its cycling scheme. NASBA can begin with either DNA or RNA and finish with either, and amplifies to 108 copies within 60 to 90 minutes. Alternatively, nucleic acid can be amplified by ligation activated transcription (LAT). LAT works from a single-stranded template with a single primer that is partially single-stranded and partially double-stranded. Amplification is initiated by ligating a cDNA to the promoter oligonucleotide and within a few hours, amplification is 108 to 109 fold. Another amplification system useful in the method of the invention is the Qxcex2 Replicase System. The Qxcex2 replicase system can be utilized by attaching an RNA sequence called MDV-1 to RNA complementary to a DNA sequence of interest. Upon mixing with a sample, the hybrid RNA finds its complement among the specimen""s mRNAs and binds, activating the replicase to copy the tag-along sequence of interest. Another nucleic acid amplification technique, ligase chain reaction (LCR), works by using two differently labeled halves of a sequence of interest which are covalently bonded by ligase in the presence of the contiguous sequence in a sample, forming a new target. The repair chain reaction (RCR) nucleic acid amplification technique uses two complementary and target-specific oligonucleotide probe pairs, thermostable polymerase and ligase, and DNA nucleotides to geometrically amplify targeted sequences. A 2-base gap separates the oligonucleotide probe pairs, and the RCR fills and joins the gap, mimicking DNA repair. Nucleic acid amplification by strand displacement activation (SDA) utilizes a short primer containing a recognition site for Hinc II with short overhang on the 5xe2x80x2 end which binds to target DNA. A DNA polymerase fills in the part of the primer opposite the overhang with sulfur-containing adenine analogs. Hinc II is added but only cuts the unmodified DNA strand. A DNA polymerase that lacks 5xe2x80x2 exonuclease activity enters at the cite of the nick and begins to polymerize, displacing the initial primer strand downstream and building a new one which serves as more primer. SDA produces greater than 107-fold amplification in 2 hours at 37xc2x0 C. Unlike PCR and LCR, SDA does not require instrumented Temperature cycling.
Another method is a process for amplifying nucleic acid sequences from a DNA or RNA template which may be purified or may exist in a mixture of nucleic acids. The resulting nucleic acid sequences may be exact copies of the template, or may be modified. The process has advantages over PCR in that it increases the fidelity of copying a specific nucleic acid sequence, and it allows one to more efficiently detect a particular point mutation in a single assay. A target nucleic acid is amplified enzymatically while avoiding strand displacement. Three primers are used. A first primer is complementary to the first end of the target. A second primer is complementary to the second end of the target. A third primer which is similar to the first end of the target and which is substantially complementary to at least a portion of the first primer such that when the third primer is hybridized to the first primer, the position of the third primer complementary to the base at the 5xe2x80x2 end of the first primer contains a modification which substantially avoids strand displacement. This method is detailed in U.S. Pat. No. 5,593,840 to Bhatnagar et al. 1997.
Finally, recent application of DNA chips or microarray technology where DNA or oligonucleotides are immobilized on small solid support may also be used to rapidly sequence sample gene and analyze its expression. Typically, high density arrays of DNA fragment are fabricated on glass or nylon substrates by in situ light-directed combinatorial synthesis or by conventional synthesis followed by immobilization (U.S. Pat. No. 5,445,934). Sample DNA or RNA may be amplified by PCR, labeled with a fluorescent tag, and hybridized to the microarray. Examples of this technology are provided in U.S. Pat. Nos. 5,510, 270 and 5,547,839, incorporated herein by reference.
The BRCA1(omi4) DNA coding sequence was obtained by end to end sequencing of the BRCA1 alleles of a subject in the manner described above followed by analysis of the data obtained. The data obtained provided a previously unpublished polymorphism.
Gene Therapy
The coding sequences can be used for gene therapy. A variety of methods are known for gene transfer, any of which might be available for use.
Direct injection of Recombinant DNA in vivo:
1. Direct injection of xe2x80x9cnakedxe2x80x9d DNA directly with a syringe and needle into a specific tissue, infused through a vascular bed, or transferred through a catheter into endothelial cells.
2. Direct injection of DNA that is contained in artificially generated lipid vesicles, or other suitable encapsulating vehicle.
3. Direct injection of DNA conjugated to a target receptor structure, such as a diptheria toxin, an antibody, or other suitable receptor.
4. Direct injection by particle bombardment, where the DNA is coated onto gold particles and shot into the cells.
This gene delivery approach involves the use of human chromosomes that have been stripped down to contain only the essential components for replication and the genes desired for transfer.
DNA is linked to a targeting molecule that will bind to specific cell-surface receptors, inducing endocytosis and transfer of the DNA into mammalian cells. One such technique uses poly-L-lysine to link asialoglycoprotein to DNA. An adenovirus is also added to the complex to disrupt the lysosomes and thus allow the DNA to avoid degradation and move to the nucleus. Infusion of these particles intravenously has resulted in gene transfer into hepatocytes.
Several vectors are used in gene therapy. Among them are the Moloney Murine Leukemia Virus (MoMLV) Vectors, the adenovirus vectors, the Adeno-Associated Virus (AAV) vectors, the retrovirus vectors, the herpes simplex virus (HSV) vectors, the poxvirus vectors, and human immunodeficiency virus (HIV) vectors.
The ideal genetic manipulation for treatment of a genetic disease would be the actual replacement of the defective gene with a normal copy of the gene. Homologous recombination is the term used for switching out a section of DNA and replacing it with a new piece. By this technique, the defective gene can be replaced with a normal gene which expresses a functioning BRCA1 tumor growth inhibitor protein.
A complete description of gene therapy can also be found in xe2x80x9cGene Therapy A Primer For Physiciansxe2x80x9d 2d Ed. by Kenneth W. Culver, M.D. Publ. Mary Ann Liebert Inc. (1996). Two Gene Therapy Protocols for BRCA1 are approved by the Recombinant DNA Advisory Committee for Jeffrey T. Holt et al. They are listed as 9602-148, and 9603-149 and are available from the NIH. The isolated BRCA1 gene can be synthesized or constructed from amplification products and inserted into a vector such as the LXSN vector. Triple strand gene repair may also be used. See U.S. Pat. Nos. 5,650,316 and 5,624,803, for example.
A BRCA1(OMI4) Polypeptide or its Functional Equivalent
It has been shown that active BRCA1 protein inhibits the growth of the cancer cells and reduces tumorigenesis. Thus, the growth of breast or ovarian cancer may be arrested or prevented by increasing the BRCA1 protein level where inadequate functional BRCA1 activity is responsible for breast or ovarian cancer. The cDNA and amino acid sequences of the BRCA1(omi4) haplotype are disclosed herein (SEQ ID No: 1 and 2, respectively). All or a fragment of the BRCA1(omi4) protein may be used in therapeutic or prophylactic treatment of breast or ovarian cancer. Such a fragment may have a similar biological function as the native BRCA1(omi4) protein or may have a desired biological function as specified below. BRCA1(omi4) polypeptides or their functional equivalents including homologous and modified polypeptide sequences are also within the scope of the present invention. Changes in the native sequence may be advantageous in producing or using the BRCA1(omi4) derived polypeptide or functional equivalent suitable for therapeutic or prophylactic treatment of breast or ovarian cancer. For example, these changes may be desirable for producing resistance against in vivo proteolytic cleavage, for facilitating transportation and delivery of therapeutic reagents, for localizing and compartmentalizing tumor suppressing agents, or for expression, isolating and purifying the target species.
There are a variety of methods to produce an active BRCA1(omi4) polypeptide or a functional equivalent as a tumor growth inhibitor. For example, one or more amino acids may be substituted, deleted, or inserted using methods well known in the art (Maniatis et al., 1982). Considerations of polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphiphathic nature of the amino acids play an important role in designing homologous polypeptide changes suitable for the intended treatment. In particular, conservative amino acid substitution using amino acids that are related in side-chain structure and charge may be employed to preserve the chemical and biological property. A homologous polypeptide typically contains at least 70% sequence homology to the native sequence. Unnatural forms of the polypeptide may also be incorporated so long as the modification retains substantial biological activity. These unnatural forms typically include structural mimics and chemical medications, which have similar three-dimensional structures as the active regions of the native BRCA1(omi4) protein. For example, these modifications may include terminal D-amino acids, cyclic peptides, unnatural amino acids side chains, pseudopeptide bonds, N-terminal acetylation, glycosylation, and biotinylation, etc. These unnatural forms polypeptide may have a desired biological function, for example, they be particularly robust in the presence of cellular or serum proteases and exopeptidases. An effective BRCA1(omi4) polypepitde or a functional equivalent may also be recognized by the reduction of the native BRCA1 protein. Regions of the BRCA1 protein may be systematically deleted to identify which regions are essential for tumor growth inhibitor activity. These smaller fragments of BRCA1(omi4) protein may then be subjected to structural and functional modification to derive the therapeutically or prophylactically effective regiments. Finally, drugs, natural products or small molecules may be screened or synthesized to mimic the function of the BRCA1 protein. Typically, the active species retain the essential three-dimensional shape and chemical reactivity, and therefore retain the desired aspects of the biological activity of the native BRCA1 protein. The activity and function of the BRCA1 protein may include transcriptional activation, granin, DNA repair, among others. Functions of the BRCA1 protein are also reviewed in Bertwistle and Ashworth, Curr. Opin. Genet. Dev. 8(1): 14-20 (1998) and Zhang et al., Cell 92:433-436 (1998). It will be apparent to one skilled in the art that a BRCA1(omi4) polypeptide or a functional equivalent may be selected because such polypeptide or functional equivalent possesses similar biological activity as the native BRCA1 protein.
Expression of the BRCA1(omi4) Protein and Polypeptide in Host Cells
All or fragments of the BRCA1(omi4) protein and polypeptide may be produced by host cells that are capable of directing the replication and the expression of foreign genes. Suitable host cells include prokaryotes, yeast cells, or higher eukaryotic cells, which contain an expression vector comprising all or a fragment of the BRCA1(omi4) cDNA sequence (SEQ. ID No: 1) operatively linked to one or more regulatory sequences to produce the intended BRCA1(omi4) protein or polypeptide. Prokaryotes may include gram negative or gram positive organisms, for example E. coli or Bacillus strains. Suitable eukaryotic host cells may include yeast, virus, and mamalian systems. For example, Sf9 insect cells and human cell lines, such as COS, MCF7, HeLa, 293T, HBL100, SW480, and HCT116 cells.
A broad variety of suitable expression vectors are available in the art. An expression vector typically contains an origin of replication, a promoter, a phenotypic selection gene (antibiotic resistance or autotrophic requirement), and a DNA sequence coding for all or fragments of the BRCA1(omi4) protein. The expression vectors may also include other operatively linked regulatory DNA sequences known in the art, for example, stability leader sequences, secretory leader sequences, restriction enzyme cleavage sequences, polyadenylation sequences, and termination sequences, among others. The essential and regulatory elements of the expression vector must be compatible with the intended host cell. Suitable expression vectors containing the desired coding and control regions may be constructed using standard recombinant DNA techniques known in the art, many of which are described in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989). For example, suitable origins of replication may include Col E1, SV4O viral and M13 origins of replication. Suitable promoters may be constitutive or inducible, for example, tac promoter, lac Z promoter, SV40 promoter, MMTV promoter, and LXSN promoter. Examples of selectable markers include neomycin, ampicillin, and hygromycin resistance and the like. Many suitable prokaryotic, viral and mammalian expression vectors may be obtained commercially, for example, from Invitrogen Corp., San Diego, Calif. or from Clontech, Palo Alto, Calif. It may be desirable that the BRCA1(omi4) protein or polypeptide is produced as a fusion protein to enhance the expression in selected host cells, to detect the expression in transfected cells, or to simplify the purification process. Suitable fusion partners for the BRCA1(omi4) protein or polypeptide are well known in the art and may include xcex2-galactosidase, glutathione-S-transferase and poly-histidine tag, among others.
Expression vectors may be introduced into host cells by various methods known in the art. The transformation procedure used depends upon the host to be transformed. Methods for introduction of vectors into host cells may include calcium phosphate precipitation, electrosporation, dextran-mediated transfection, liposome encapsulation, nucleus microinjection, and viral or phage infection, among others.
Once an expression vector has been introduced into a suitable host cell, the host cell may be cultured under conditions permitting expression of large amounts of the BRCA1(omi4) protein or polypeptide. The expression product may be identified by many approaches well known in the art, for example, sequencing after PCR-based amplification, hybridization using probes complementary to the desired DNA sequence, the presence or absence of marker gene functions such as enzyme activity or antibiotic resistance, the level of mRNA production encoding the intended sequence, immunological detection of a gene product using monoclonal and polyclonal antibodies, such as Western blotting or ELISA. The BRCA1(omi4) protein or polypeptides produced in this manner may then be isolated following cell lysis and purified using various protein purification techniques known in the art, for example, ion exchange chromatography, gel filtration chromatography and immunoaffinity chromatography.
It is generally preferred that whenever possible, longer fragments of BRCA1(omi4) protein or polypeptide are used, particularly to include the desired functional domains of BRCA1 protein. Expression of shorter fragments of DNA may be useful in generating BRCA1(omi4) derived immunogen for the production of anti-BRCA1(omi4) antibodies. It should, of course, be understood that not all expression vectors, DNA regulatory sequences or host cells will function equally well to express the BRCA1(omi4) protein or polypeptides of the present invention. However, one of ordinary skill in the art may make a selection among expression vectors, DNA regulatory sequences, host cells, and codon usage in order to optimize expression using known technology in the art without undue experimentation. Studies of the BRCA1 protein and examples of genetic manipulation of the BRCA1 protein are summarized in two recent review articles, Bertwistle and Ashworth, Curr. Opin. Genet. Dev. 8(1): 14-20 (1998) and Zhang et al., Cell 92:433-436 (1998).
In Vitro Synthesis and Chemical Synthesis
Although it is preferred that the BRCA1(omi4) protein or polypeptides be obtained by overexpression in prokaryotic or eukaryotic host cells, the BRCA1(omi4) polypeptides or their functional equivalents may also be obtained by in vitro translation or synthetic means by methods known to those of ordinary skill in the art. For example, in vitro translation may employ a mRNA encoded by a DNA sequence coding for all or fragments of the BRCA1(omi4) protein or polypeptides. Chemical synthesis methodology such as solid phase synthesis may be used to synthesize a BRCA1(omi4) polypeptide structural mimic and chemically modified analogs thereof. The polypeptides or the modifications and mimic thereof produced in this manner may then be isolated and purified using various purification techniques, such as chromatographic procedures including ion exchange chromatography, gel filtration chromatography and immunoaffinity chromatography.
Protein Replacement Therapy
The ability of the BRCA1 protein to inhibit tumor growth demonstrates that various BRCA1 protein targeted therapies may be utilized in treating and preventing tumors in breast and ovarian cancer. The present invention therefore includes therapeutic and prophylactic treatment of breast and ovarian cancer using therapeutic pharmaceutical compositions containing the BRCA1(omi4) protein, polypeptides, or their functional equivalents. For example, protein replacement therapy may involve directly administering the BRCA1(omi4) protein, a BRCA1(omi4) polypeptide, or a functional equivalent in a pharmaceutically effective carrier. Alternatively, protein replacement therapy may utilize tumor antigen specific antibody fused to the BRCA1(omi4) protein, a polypeptide, or a functional equivalent to deliver anti-cancer regiments specifically to the tumor cells.
To prepare the pharmaceutical compositions of the present invention, an active BRCA1(omi4) protein, a polypeptide, or its functional equivalent is combined with a pharmaceutical carrier selected and prepared according to conventional pharmaceutical compounding techniques. A suitable amount of the composition may be administered locally to the site of a tumor or systemically to arrest the proliferation of tumor cells. The methods for administration may include parenteral, oral, or intravenous, among others according to established protocols in the art.
Pharmaceutically acceptable solid or liquid carriers or components which may be added to enhance or stabilize the composition, or to facilitate preparation of the composition include, without limitation, syrup, water, isotonic solution, 5% glucose in water or buffered sodium or ammonium acetate solution, oils, glycerin, alcohols, flavoring agents, preservatives, coloring agents, starches, sugars, diluents, granulating agents, lubricants, binders, and sustained release materials. The dosage at which the therapeutic compositions are administered may vary within a wide range and depends on various factors, such as the stage of cancer progression, the age and condition of the patient, and may be individually adjusted.
Diagnostic Reagents
The BRCA1(omi4) protein, polypeptides, their functional equivalents, antibodies, and polynucleotides may be used in a wide variety of ways in addition to gene therapy and protein replacement therapy. They may be useful as diagnostic reagents to measure normal or abnormal activity of BRCA1 at the DNA, RNA and protein level. The present invention therefore encompasses the diagnostic reagents derived from the BRCA1(omi4) cDNA and protein sequences as set forth in SEQ. ID. Nos: 1 and 2 respectively. These reagents may be utilized in methods for monitoring disease progression, for determining patients suited for gene and protein replacement therapy, or for detecting the presence or quantifying the amount of a tumor growth inhibitor following such therapy. Such methods may involve conventional histochemical techniques, such as obtaining a tumor tissue from the patient, preparing an extract and testing this extract for tumor growth or metabolism. For example, the test for tumor growth may involve measuring abnormal BRCA1(omi4) activity using conventional diagnostic assays, such as Southern, Northern, and Western blotting, PCR, RT-PCR, immunoassay, and immunoprecipitation. In biopsies of tumor tissues, the loss of the BRCA1(omi4) expression in tumor tissue may be verified by RT-PCR and Northern blotting at the RNA level. A Southern blot analysis, genomic PCR, or fluorescence in situ hybridization (FISH) may also be performed to examine the mutations of BRCA1 at the DNA level. And, a Western blotting, protein truncation assay, or immunoprecipitation may be utilized to analysis the effect at the protein level.
These diagnostic reagents are typically either covalently or non convalently attached to a detectable label. Such a label includes a radioactive label, a calorimetric enzyme label, a fluorescence label, or an epitope label. Frequently, a reporter gene downstream of the regulatory sequences is fused with the BRCA1(omi4) protein or polypeptide to facilitate the detection and purification of the target species. Commonly used reporter genes in BRCA1 fusion proteins include xcex2-galactosidase and luciferase gene.
The BRCA1(omi4) protein, polypeptides, their functional equivalents, antibodies, and polynucleotides may also be useful in the study of the characteristics of the BRCA1 protein, such as structure and function of BRCA1 in oncogenesis or subcellular localization of the BRCA1 protein in normal and cancerous cells. For example, yeast two-hybrid system has been frequently used in the study of cellular function of BRCA1 to identify the regulator and effector of BRCA1 growth control pathways (See reviews of Bertwistle and Ashworth, 1998 and Zhange et al., 1998). In addition, the BRCA1(omi4) protein, polypeptides, their functional equivalents, antibodies, and polynucleotides may also be used in in vivo cell based and in vitro cell free assays to screen natural products and synthetic compounds which may mimic, regulate or stimulate BRCA1 protein function.
Antisense Inhibition
Antisense suppression of endogenous BRCA1 expression may assess the effect of the BRCA1 protein on cell growth inhibition using known method in the art (Crooke, Annu. Rev. Pharmacol. Toxicol. 32:329-376 (1992) and Robinson-Benion and Holt, Methods Enzymol. 254:363-375 (1995)). Given the cDNA sequence as set forth in SEQ ID. NO: 1, one of skill in the art can readily obtain anti-sense strand of DNA and RNA sequences to interfere with the production of the wild-type BRCA1(omi4) protein or the mutated form of BRCA1 protein. Alternatively, antisense oligonucleotide may be designed to target the control sequences of BRCA1(omi4) gene to reduce or prevent the expression of the endogenous BRCA1(omi4) gene. Examples of using oligonucleotide-based antisense technology to inhibit the BRCA1 expression are provided in Husain et al., Cancer Res. 58:1120-1123 (1998).
Antibodies
The BRCA1(omi4) protein, polypeptides, or their functional equivalent may be used as immunogens to prepare polyclonal or monoclonal antibodies capable of binding the BRCA1 derived antigens in a known manner (Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1988). These antibodies may be used for the detection of the BRCA1 protein, polypeptides, or a functional equivalent in an immunoassay, such as ELISA, Western blot, radioimmunoassay, enzyme immunoassay, and immunocytochemistry. Typically, an anti-BRCA1 antibody is in solution or is attached to a solid surface such as a plate, a particle, a bead, or a tube. The antibody is allowed to contact a biological sample or a blot suspected of containing the BRCA1 protein or polypeptide to form a primary immunocomplex. After sufficient incubation period, the primary immunocomplex is washed to remove any non-specifically bound species. The amount of specifically bound BRCA1 protein or polypeptide may be determined using the detection of an attached label or a marker, such as a radioactive, a fluorescent, or an enzymatic label. Alternatively, the detection of BRCA1 derived antigen is allowed by forming a secondary immunocomplex using a second antibody which is attached with a such label or marker. The antibodies may also be used in affinity chromatography for isolating or purifying the BRCA1 protein, polypeptides or their functional equivalents. Examples of preparing and using anti-BRCA1 antibodies are provided in Ruffner et al., Proc. Natl. Acad. Sci. USA 94:7138-7143 (1997) and Jensen et al., Nat. Genetics 12:303-308 (1996).